A procedure for automated low uncertainty assessment of empty cavity mode frequencies in Fabry-Pérot cavity based refractometry that does not require access to laser frequency measuring instrumentation is presented. It requires a previously well-characterized system regarding mirror phase shifts, Gouy phase, and mode number, and is based on the fact that the assessed refractivity should not change when mode jumps take place. It is demonstrated that the procedure is capable of assessing mode frequencies with an uncertainty of 30 MHz, which, when assessing pressure of nitrogen, corresponds to an uncertainty of 0.3 mPa.